NEWS

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diaQTL 1.10

• Fixed h2 output for binary traits

diaQTL 1.09

• fixed bug in phased_parents for diploids

diaQTL 1.08

• fixed error in convert_rabbit regarding parental haplotype naming

diaQTL 1.07

• new function haplo_match to match up haplotypes between two phased parent files

diaQTL 1.06

• null model for scan1 did not include the covariate; fixed now

diaQTL 1.05

• Removed NA before running BGLR to avoid NA for DIC

diaQTL 1.04

• Fixed error introduced in 1.02 for fitQTL

diaQTL 1.03

• No longer assumes first column in phenotype file is named "id"

diaQTL 1.02

• Matrix objects cast to base matrix class to prevent error with BGLR
• Fixed error with dominance=1 in fitQTL

diaQTL 1.01

• Separate tmp directories used in scan1 to prevent problems with parallel execution on some machines

diaQTL 1.00

• Added epistasis to IBDmat
• Renamed cofactor argument to covariate for scan1

diaQTL 0.99

• Changed function name to convert_polyorigin
• Renamed polyorigin slot as "input"
• Proportion of variance computed based on clone rather than plot average

diaQTL 0.98

• Updated documentation
• Fixed scan1_summary plot's flip and threshold arguments
• Fixed set_params output. The help does not save it in a par1 object anymore

diaQTL 0.97

• Added read_rabbit function for diploids

diaQTL 0.96

• Added outstem option to read_polyancestry
• New arguments for fitQTL to allow multiple QTL and epistasis
• Added kinship matrices to diallel_geno class, computed in read_data, for faster fiTQTL
• Renamed qtl1 as runBGLR
• Changed set_params to return results for each genetic variance component
• Changed scan1 and set_params to call fitQTL for better code stewardship

diaQTL 0.95

• Updated scan1_summary for default statistic as deltaDIC
• Added marker position in fine_map
• Replaced LODthresh with DIC_thresh
• Added alpha parameter for DIC_thresh
• Fixed all the notes for R checking
• Updated vignette in terms of deltaDIC

diaQTL 0.94

• Changed default value for dominance in read_data to 4
• Updated vignette

diaQTL 0.93

• Added new cofactor functionality to fitQTL
• Removed Gprep function
• Added n.core option for IBDmat

diaQTL 0.92

• Modified permutation test to preserve relationship between phenotypes and fixed effects
• Modified cofactor functionality in scan1 to include additive x additive epistasis
• Modified scan1_summary so that either DIC or LOD can be used

diaQTL 0.91

• Updates to fine_map
• Switched from mclapply to parLapply for Windows compatibility

diaQTL 0.90

• Added constraint that sum of qtl effects (for each order) is zero
• Inclusion of CI for fitQTL is now optional

diaQTL 0.89

• Changed R2 to r2

diaQTL 0.88

• Modified haplo_switch to become fine_map
• Added bioRxiv citation

diaQTL 0.87

• Modified haplo_unique to become haplo_cluster

diaQTL 0.86

• Removed valents_summary
• Added digenic model to LODthresh
• Updated potato dataset

diaQTL 0.85

• Modified haplo_freq plot, now returns frequency of individuals
• Fixed read_polyancestry to handle degenerate case of 1 pop with 1 chrom
• Added functions phased_parents and haplo_unique

diaQTL 0.84

• Added function valents_summary

diaQTL 0.83

• Added polygenic effect to fitQTL

diaQTL 0.82

• Check whether marker is valid in set_params
• Updated recommendation for set_params

diaQTL 0.81

• Added function BayesCI
• cM no longer optional

diaQTL 0.80

• modified interface for set_params
• merged Amat and Dmat into IBDmat
• fitQTL returns residuals
• fitQTL returns Bayesian CI
• Changed color scheme for fitQTL plots
• Dominance plot from fitQTL has dom above diagonal, add + dom below diagonal

diaQTL 0.79

• Cosmetic change to scaling of GCA

diaQTL 0.78

• Fixed bug in read_polyancestry
• explicitly set stringsAsFactors = T when reading phenofile
• Fixed tmp directory issue

diaQTL 0.77

• Changed terminology from "haplotype.pairs" to "diplotypes"
• Added functions to get and plot diplotype dosage
• Added function to create input files from PolyOrigin output file
• Changed formatting of output for fitQTL
• BGLR output files now put in tmp directory

diaQTL 0.76

• Adjusted frequency in haplo_freq by ploidy

diaQTL 0.75

• Can now include multiple markers in haplo_plot
• Fixed labeling error in fitQTL plot for diploids
• Fixed error with dominance effects for diploids

diaQTL 0.74

• scan1 output now includes all markers, not just bins
• Added function haplo_freq
• Changed name of haplotypes function to haplo_get

diaQTL 0.73

• Corrected error with names for digenic effects

diaQTL 0.72

• Corrected error introduced in v0.71

diaQTL 0.71

• Fixed documentation for set_params

diaQTL 0.70

• Changed terminology from allele to haplotype
• Added function haplo_switch
• Changed name of dosage to haplotypes
• Changed name of plot_dosage to haplo_plot
• Added marker binning to reduce run time
• Both cM and bp positions can be used
• Added trigenic and quadrigenic dominance
• Added parallel execution in read_data
• Changed linear model
• Removed "population" from pedigree input file

diaQTL 0.63

• Fixed error with peak position units in scan1_summary

diaQTL 0.62

• Fixed error with plot_dosage for S1 individuals
• Removed default option for "distance" argument in plotting

diaQTL 0.61

• Changed "distance" to "position" in plot_dosage and scan1_summary

diaQTL 0.60

• Repository is public
• Removed option to disable dominance in read_data
• Removed qqplot and dominance option from set_params
• Changed reporting of dominance variance to be proportion of total variance
• Added LODthresh function
• Removed two markers from the vignette dataset due to discordance with new reference genome
• Changed display of R2 results to percent instead of proportion
• Removed deltaDIC from scan1_summary
• fitQTL returns h2 and d2 as named vector instead of list
• Changed sign of phenotype data
• Changed indiv to id